biojava · josemduarte · May 7, 2019 · May 7, 2019 · May 7, 2019 · May 7, 2019
diff --git a/README.md b/README.md
@@ -1,18 +1,18 @@
  <img src="logo.png" height="30"/> Tutorial
 ===
 
-A brief introduction into [BioJava](https://github.com/biojava/biojava).
+A brief introduction into [BioJava](https://www.biojava.org).
 -----
 
-The goal of this tutorial is to provide an educational introduction into some of the features that are provided by BioJava.
+The goal of this tutorial is to provide an educational introduction into some of the features that are provided by BioJava. This tutorial is still under development, hence not yet comprehensive for the entire library. Please also check other sources of [documentation](https://biojava.org/wiki/Documentation).
 
-At the moment this tutorial is still under development. Please check  the [BioJava Cookbook](http://biojava.org/wikis/BioJava:CookBook4.0) for a more comprehensive collection of examples about what is possible with BioJava and how to do things.
+The examples within the tutorial are intended to work with the most recent version of BioJava, although most examples will work with BioJava 3.0 and higher. Please do submit a [new issue](https://github.com/biojava/biojava-tutorial/issues) if you find any problems.
 
-The tutorial is intended to work with the most recent version of BioJava, although most examples will work with BioJava 3.0 and higher.
+The tutorial is subdivided into several books, corresponding to the respective BioJava modules. Each book is further subdivided into several chapters that intend to describe the main functionality of the module in order of increasing complexity.
 
 ## Index
 
-Quick [Installation](installation.md)
+[Quick Installation](installation.md)
 
 Book 1: [The Core Module](core/README.md), basic working with sequences.
 
@@ -28,16 +28,14 @@ Book 6: [The ModFinder Module](modfinder/README.md), identifying potein modifica
 
 ## License
 
-The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
-
-[view license](license.md)
+The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
 
 ## Please Cite
 
-**BioJava: an open-source framework for bioinformatics in 2012**<br/>
-*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
-[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
+[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)
 
 
 <!--automatically generated footer-->
diff --git a/alignment/README.md b/alignment/README.md
@@ -36,19 +36,16 @@ Chapter 5 - Reading and writing of multiple alignments
 
 Chapter 6 - BLAST - why you don't need BioJava for parsing BLAST
 
-## Please cite
-
-**BioJava: an open-source framework for bioinformatics in 2012**<br/>
-*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
-[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
-
-
 ## License
 
-The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
+The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](../license.md).
+
+## Please cite
 
-[view license](../license.md)
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
+[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)
 
 
 

diff --git a/core/README.md b/core/README.md
@@ -32,19 +32,16 @@ Chapter 3 - [Reading and Writing sequences](readwrite.md)
 
 Chapter 4 - [Translating](translating.md) DNA and protein sequences.
 
-## Please cite
-
-**BioJava: an open-source framework for bioinformatics in 2012**<br/>
-*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
-[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
-
-
 ## License
 
-The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
+The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
+
+## Please Cite
 
-[view license](../license.md)
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
+[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)
 
 
 

diff --git a/genomics/README.md b/genomics/README.md
@@ -39,19 +39,16 @@ Chapter 5 - Reading [karyotype (cytoband)](karyotype.md) files
 Chapter 6 - Reading genomic DNA sequences using UCSC's [.2bit file format](twobit.md)
 
 
-## Please cite
-
-**BioJava: an open-source framework for bioinformatics in 2012**<br/>
-*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
-[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
-
-
 ## License
 
-The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
+The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
+
+## Please Cite
 
-[view license](../license.md)
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
+[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)
 
 
 

diff --git a/modfinder/README.md b/modfinder/README.md
@@ -27,24 +27,21 @@ Chapter 3 - [How to identify protein modifications in a structure](identify-prot
 
 Chapter 4 - [How to define a new protein modification](add-protein-modification.md)
 
-## Please cite
+## License
+
+The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
+
+## Please Cite
 
 **BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank**<br/>
 *Jianjiong Gao; Andreas Prlic; Chunxiao Bi; Wolfgang F. Bluhm; Dimitris Dimitropoulos; Dong Xu; Philip E. Bourne; Peter W. Rose* <br/>
 [Bioinformatics. 2017 Feb 17.](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx101) <br/>
 [![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtx101-blue.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btx101) [![pubmed](http://img.shields.io/badge/pubmed-28334105-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/28334105)
 
-**BioJava: an open-source framework for bioinformatics in 2012**<br/>
-*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
-[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
-
-
-## License
-
-The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
-
-[view license](../license.md)
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
+[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)
 
 
 

diff --git a/protein-disorder/README.md b/protein-disorder/README.md
@@ -92,18 +92,16 @@ Map<FastaSequence, Range[]> ranges = Jronn.getDisorder(sequences);
 
 ```
 
-## Please cite
-
-**BioJava: an open-source framework for bioinformatics in 2012**<br/>
-*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
-[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
-
 ## License
 
-The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
+The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
+
+## Please Cite
 
-[view license](../license.md)
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
+[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)
 
 
 

diff --git a/structure/README.md b/structure/README.md
@@ -64,22 +64,16 @@ Chapter 17 - [Special Cases](special.md)
 Chapter 18 - [Lists](lists.md) of PDB IDs and PDB [Status Information](lists.md)
 
 
-### Author: 
-
-[Andreas Prli&#263;](https://github.com/andreasprlic)
-
-## Please cite
-
-**BioJava: an open-source framework for bioinformatics in 2012**<br/>
-*Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
-[Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
-
 ## License
 
-The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license.
+The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](license.md).
+
+## Please Cite
 
-[view license](../license.md)
+**BioJava 5: A community driven open-source bioinformatics library**<br/>
+*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
+[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)
 
 
 

diff --git a/structure/symmetry.md b/structure/symmetry.md
@@ -235,6 +235,15 @@ QuatSymmetryResults overallResults = QuatSymmetryDetector.getGlobalSymmetry(s, p
 See also the [test](https://github.com/biocryst/biojava/blob/df22da37a86a0dba3fb35bee7e17300d402ab469/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/symmetry/TestQuatSymmetryDetectorExamples.java#L167-L192) provided in **BioJava** for a real case working example.
 
 
+## Please Cite
+
+**Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm**<br/>
+*Spencer E Bliven, Aleix Lafita, Peter W Rose, Guido Capitani, Andreas Prlić, & Philip E Bourne* <br/>
+[PLOS Computational Biology (2019) 15 (4):e1006842.](https://journals.plos.org/ploscompbiol/article/citation?id=10.1371/journal.pcbi.1006842) <br/>
+[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006842-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006842) [![pubmed](https://img.shields.io/badge/pubmed-31009453-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/31009453)
+
+
+
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